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Majority-rule consensus tree inferred from Bayesian analysis of ITS data. Posterior probability values are indicated above branches, ML bootstrap values below. Values below 50% are not shown.

Majority-rule consensus tree inferred from Bayesian analysis of ITS data. Posterior probability values are indicated above branches, ML bootstrap values below. Values below 50% are not shown.

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Despite being one of the larger genera of Caryophyllaceae with about 60 cushion-forming subshrubby species, Acanthophyllum is represented poorly in previous molecular phylogenetic studies. The genus is an important component of the subalpine steppe flora in Central to Southwest Asia. Although the placement of Acanthophyllum in the tribe Caryophylle...

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... and discussed in detail, whereas those of ML and MP analyses including tree length, invariable characters, number of infor- mative characters, number of indels, consistency and retention indices, and likelihood bootstraps are summarized in Table 2 and Figs. 4-5. Two major well-supported clades are recognized within Acanthophyllum in both the ITS (Fig. 4) and the rps16 (Fig. 5) trees. These clades are congruent with the Clades I and II ob- tained by *BEAST species tree analysis. The genera Ochotono­ phila, Scleranthopsis, Diaphanoptera (pro majora parte) and one species of Gypsophila are nested within Acanthophyllum. However, Allochrusa is sister to Acanthophyllum in the ITS phylogeny ...
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... 4) and the rps16 (Fig. 5) trees. These clades are congruent with the Clades I and II ob- tained by *BEAST species tree analysis. The genera Ochotono­ phila, Scleranthopsis, Diaphanoptera (pro majora parte) and one species of Gypsophila are nested within Acanthophyllum. However, Allochrusa is sister to Acanthophyllum in the ITS phylogeny (PP 0.86; Fig. 4), whereas it nests within Acantho­ phyllum Clade II in the rps16 phylogeny (PP 1.0; Fig. 5). Clade I is composed of A. sect. Oligosperma, sect. Pleiosperma, sect. Scapiflora, sect. Pseudacanthophyllum, sect. Macrostegia and sect. Macrodonta. Clade I also contains representatives of the genera Diaphanoptera, Ochotonophila, ...
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... Acanthophyllum, i.e., Scleranthopsis, Ochotonophila and Diaphanoptera, were ignored. In our trees these small genera are embedded in Acanthophyllum s.l. (Figs. 4-5). Cushion- forming subshrubby to somewhat woody habit is a character that distinguishes the Acanthophyllum s.l. clade (Acanthophyl­ lum, Scleranthopsis, Allochrusa, Ochotonophila, Diaphanop­ tera p.p.) from the rest of tribe Caryophylleae. We conclude that the morphological characters used for delimiting Acan­ thophyllum s.str., ...
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... analyses of nuclear and plastid loci show that the Acan­ thophyllum s.l. clade (including Allochrusa, Ochotonophila, Diaphanoptera p.p. and Scleranthopsis), (PP 1.0; Figs. 4-5) is sister to a clade holding Dianthus and Petrorhagia (and Vele­ zia only in ITS tree) (PP 1.0; Figs. 4-5). This is in agreement with previous studies (Fior & al., 2006;Harbaugh & al., 2010;Valente & al., 2010;Greenberg & Donoghue, 2011). Gypsophila cerastioides nests within Acanthophyllum ...
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... taxa with more than eight ovules. How- ever, the support for clade E is not strong and is due only to rps16 (PP 0.98; Fig. 5). The placement of D. ekbergii as sister to A. sects. Pseudacanthophyllum and Scapiflora is likewise poorly supported in the species tree (PP 0.91; Fig. 3) and the rps16 tree (PP 0.68; Fig. 5) and not at all in the ITS tree (Fig. 4), where it is resolved as sister to Gypsophila cerastioides. We were not successful in generating high-quality sequences for D. khorassanica, the type of the genus. Therefore, the delimi- tation of Diaphanoptera from Acanthophyllum, Gypsophila and Ochotonophila cannot be ascertained, but it is clear that Diaphanoptera as currently ...
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... both analyses of ITS and rps16 (Figs. 4-5) G. cerasti­ oides falls within Acanthophyullum s.l. Gypsophila muralis resolves as sister to the Dianthus-Petrorhagia clade in the ITS tree (consistent with Greenberg & Donoghue, 2011), and the remaining species of Gypsophila are found in two additional clades. This shows that Gypsophila is non-monophyletic. A broad molecular study ( ...
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... tree (Fig. 3), despite mor- phological differences that make them easily recognizable. Species of A. sect. Scapiflora have elongated, leafless pedun- cles whereas species of A. sect. Pseudacanthophyllum have a condensed habit with the inflorescence set close to the leaves. The two sections are, however, resolved as monophyletic in the ITS tree (Fig. 4). It will require sampling of other nuclear loci to resolve whether the incongruence should be attributed to stochasticity or needs a biological ...
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... 3) has poor support but is more or less identical to the large and taxonomically complicated A. sect. Oligosperma (except for A. caespitosum which is resolved as member of Clade II in all analyses). However, without A. andarabicum Podl. ex Schiman-Czeika, the rest of the clade (clade L) has strong sup- port in all trees. Only the ITS phylogeny (Fig. 4) has strong support (PP 1.0) for clade K. Schischkin (1936) divided A. sect. Oligosperma into five series. Series Elatiora Schischk. (including A. elatius Bunge and A. borsczowii Litv.) was later elevated to sectional rank (Zakirov & Musaeva, 1981). However, Schiman-Czeika (1988) included A. elatius and A. borsczowii within sect. ...
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... elatius Bunge and A. borsczowii Litv.) was later elevated to sectional rank (Zakirov & Musaeva, 1981). However, Schiman-Czeika (1988) included A. elatius and A. borsczowii within sect. Oligosperma. We can confirm the latter opinion, as A. borsczowii falls within the core group of A. sect. Oligosperma in the species (PP 0.96; Fig. 3), ITS (PP 1.0; Fig. 4) and rps16 (PP 1.0; Fig. 5) ...

Citations

... Especially Dianthus and Acanthophyllum C.A.Mey. are the most approved genus as monophyletic tribe of Caryophyllaceae family via morphological and molecular data (Fior et al., 2006;Harbaugh et al., 2010;Pirani et al., 2014). Moreover, for that reason, synonyms are still needed to make the Dianthus completely monophyletic (Greenberg and Donoghue, 2011;Harbaugh et al., 2010;Hamzaoğlu et al., 2021). ...
... Due to its different morphological features within the Caryophyllaceae family, the genus Dianthus has always been problematic among differentiation of the genus species. Thus, molecular analysis mostly made clear view for these studies (Fior et al., 2006;Harbaugh et al., 2010;Pirani et al., 2014). For instance, Hamzaoğlu et al. (2021) studied on the genus Dianthus to describe new species D. yilmazii with both morphological characters and molecular data. ...
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Dianthus berkayii belongs to sect. Fimbriati was described and illustrated as a new species from Erzincan Province in Eastern Anatolia, Turkey. In the current study morphological, palynological, and molecular characters were compared and discussed with its closely related species. The new species is similar to D. crinitus with fimbriate corolla, linear, acuminate, ± rigid leaves. Also similar to D. vanensis with fimbriate corolla, linear, acuminate, ± rigid, curved divaricate leaves. But distinctly different from D. crinitus by having linear and curved divaricate leaves, stem with 3–4(–5) internodes (not 5–8), a style much longer than petals, and different from D. vanensis with narrower leaves, ebarbulate and long fimbriate corolla. The bracts of D. berkayii are 1/3 of the length of the calyx, but not equal to the calyx length. The IUCN threat category of D. berkayii was determined to be “CR (Critically Endangered)” therewithal it is an Irano-Turanian element. In the study, the geographical distributions of D. berkayii, D. crinitus, and D. vanensis are also mapped, the identification key of these species was provided, pollen morphology and phylogenetic analyses based on ITS region of rDNA and ecological notes are also presented.
... DNA extraction, amplification, and sequencing. -The selected taxa were sequenced for their nuclear ribosomal internal transcribed spacer (nrITS) and the plastid rps16 gene, known as the most informative and effective molecular markers in phylogenetic inference of Caryophyllaceae (Oxelman & Petri, 2011;Pirani & al., 2014;Sadeghian & al., 2015;Madhani & al., 2018). A total of 82 and 83 sequences were generated for nrDNA ITS and cpDNA rps16, respectively. ...
Article
The tribe Alsineae is a large monophyletic group in the family Caryophyllaceae especially found across Eurasia and the Americas, but with a center of diversity in the Mediterranean region. Several previous molecular phylogenetic studies have focused on the delimitation of genera and tribes of Caryophyllaceae, especially the subfamily Alsinoideae or the tribe Alsineae in a broader sense than now recognized. However, there are still many open questions regarding the subdivision of the tribe and genus delimitation. In the present study, we sampled 191 (148 species) and 149 (125 species) accessions of Alsineae representing almost all (Adenonema and Pseudocerastium were not available to us) recognized genera in the tribe for nuclear DNA internal transcribed spacer (ITS) and plastid marker rps16 sequences, respectively. A combined matrix of 103 species was built for taxa with both sequences available. Maximum parsimony and Bayesian inference analyses retrieved Cerastium and Stellaria (including Myosoton) as the largest monophyletic genera, while other genera were medium‐sized (10–20 spp.) or small (<10 spp.). Our expanded sampling of Pseudostellaria and its relatives suggests a broader circumscription of this genus. Major divergence in morphology, particularly of the seeds, observed in the “Protostellaria”‐clade, allows recognition of some taxonomic changes. A total of 16 genera are recognized in Alsineae including Cerastium, Dichodon, Hartmaniella, Holosteum, Lepyrodiclis, Mesostemma, Moenchia, Nubelaria, Odontostemma, Pseudostellaria, Rabelera, Schizotechium, Shivparvatia, and Stellaria, along with Adenonema and Pseudocerastium that could not be analyzed and are, therefore, kept as distinct genera. A diagnostic key to these genera, as well as notes on their relationships, distribution, and nomenclature, is provided.
... The Caryophyllaceae family is subdivided into three subfamilies, ie. Caryophylloideae, Alsinoideae, and Paronychioideae (Greenberg and Donoguhe 2011;Pirani et al. 2014;Hernandez-Ledesma et al. 2015). The Caryophyllaceae has a worldwide distribution, and this family is diverse. ...
... Acanthophyllum Meyer plant species are shrubs and perennial. The majority of Acanthophyllum occurs in Iran and Central Asian countries (Ghaffari 2004;Pirani et al. 2014;Mahmoudi Shamsabad et al. 2020). The Caryophyllaceae family is a complex taxonomical family. ...
... The species of the genus Allochrusa were considered once as members of Acanthophyllum subgenus. Allochrusa (Schischkin 1936) and molecular phylogenetic studies by Madhani et al. (2018) corroborate the taxonomic treatment performed by Pirani et al. (2014) and contradict the treatment by Hernandez-Ledesma et al. (2015), where it was recognized provisionally at the generic level. According to this concept, it is necessary to resurrect the generic name Acanthophyllum for some taxa treated as Allochrusa in recent taxonomic surveys . ...
Article
The Caryophyllaceae family is complex. Several attempts have been carried out in the past to study Caryophyllaceae members. This study mainly focused on Allochrusa Bunge to determine its genetic structure and used ISSR markers, ITS, and rps16 data to classify and differentiate Allochrusa species. We collected 122 Allochrusa specimens. Our analysis included morphological and molecular method approaches. Morphometry analysis indicated that floral characters could assist in the identification of Allochrusa species. A. persica (Boiss.) Boiss. and A. versicolor Fisch. & C.A.Mey. showed affinity to each other. A. bungei Boiss. formed a separate group. Analysis of molecular variance showed significant genetic differentiation in Allochrusa (p= 0.001). The majority of genetic variation was among the Allochrusa population. We recorded minimum gene flow (Nm=0.176) between Allochrusa species. Besides this, isolation by distance occurs in Allochrusa members, as shown in the Mantel test result (r = 0.01, p = 0.0002). STRUCTURE analysis revealed three genetic groups. It is evident that A. persica, A. versicolor, and A. bungei differ genetically from each other. Our current findings have implications in plant systematics and biodiversity management.
... The monophyly of tribe Caryophylleae and some of its large genera such as Dianthus and Acanthophyllum C.A.Mey. are confirmed by both morphological and molecular evidence (Fior et al. 2006;Harbaugh et al. 2010;Pirani et al. 2014). However, some transfers and synonymy are still necessary to make the genus Dianthus entirely monophyletic (Greenberg & Donoghue 2011;Harbaugh et al. 2010). ...
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Dianthus yilmazii is a new species of Dianthus (Caryophyllaceae) found during a botanical trip to Kayseri, Turkey, in July 2017. Its description, images, distribution, ecology and threat category are provided. It is compared with the closely related species, Dianthus crinitus and D. erythrocoleus based on its general morphology. The relationships between the new species and its close relatives were determined based on ITS sequences.
... Four of the six species have been sampled in recent phylogenetic studies of Caryophyllaceae. Pirani & al. (2014) revealed that Diaphanoptera in its traditional concept is not monophyletic and includes at least two phylogenetically distinct groups. However, D. khorasanica, the type of the genus, was not included in that study, rendering the phylogenetic position of the genus unresolved. ...
... However, some authors reduced Allochrusa to an infrageneric taxon within Acanthophyllum (e.g., Golenkin, 1893;Schischkin, 1936). Pirani & al. (2014) sampled three Allochrusa species (including the type, Al. versicolor (Fisch. & C.A.Mey.) ...
... Oligosperma are confusing, and a few species of the section have overlapping features. This taxonomic complexity was reflected in the previous study of the group (Pirani & al., 2014), in which internal relationships within the section were not satisfactorily resolved using ITS and rps16 data. The latter study concluded that a more extensive sampling of the section might help resolve the species. ...
Article
The generic boundary of the broadly defined Acanthophyllum s.l., the third‐largest genus of the tribe Caryophylleae (Caryophyllaceae), has been a subject of taxonomic confusion. Acanthophyllum s.l. now includes five minor genera previously recognized as independent. Among these small genera, the inclusion of Allochrusa, Ochotonophila, and Scleranthopsis within Acanthophyllum s.l. was confirmed by previous molecular studies, while the positions of Diaphanoptera and Kuhitangia remained uncertain. We have performed an updated molecular study of Acanthophyllum s.l. including an increased sampling of the genera and sections assigned to this group, using intron sequences of the chloroplast gene rps16 and nuclear ribosomal internal transcribed spacer (ITS) sequences. Cyathophylla, Heterochroa, and Saponaria were chosen as outgroups for performing phylogenetic analyses using maximum likelihood and Bayesian methods. The present results suggest that, in addition to the genera mentioned above, both Diaphanoptera and Kuhitangia should also be synonymized within Acanthophyllum. Sections Diaphanoptera, Kuhitangia and Pseudomacrostegia are introduced as new infrageneric taxa within Acanthophyllum. Our results also indicate that some annual species of Saponaria are closely related to Acanthophyllum.
... DNA extraction and amplification. -Two DNA fragments, extensively used to trace the phylogeny of Caryophyllaceae (e.g., Oxelman & Lidén, 1995;Oxelman & al., 1997;Pirani & al., 2014;Sadeghian & al., 2015;Madhani & al., 2018), were selected for comparative sequencing, i.e., the internal transcribed spacer (ITS) region of the nuclear ribosomal cistron (consisting of ITS1, the intervening 5.8S gene, and ITS2) and the intron of the plastid gene rps16. DNA was extracted from fresh or herbarium materials using a NucleoSpin Plant DNA extraction kit (Macherey-Nagel, Düren, Germany) according to the manufacturer's protocol. ...
Article
The systematization of species in plant taxonomy based on the phylogenetic relationships among them are of utmost importance and also very challenging in large genera. In those, phylogenetic results often may suggest substantially different relationships than previous classifications, and call for large‐scale taxonomic revisions. Delimitation of the genus Silene has been and is still somewhat controversial, and recent molecular phylogenetic studies have settled several monophyletic groups that differ substantially from previous taxonomies. The infrageneric taxonomy of Silene s.str. has not been updated as a whole taking the phylogenetic information into account. In this study, we review previous phylogenetic results based on multiple loci, and conducted comprehensive gene tree analyses based on the nrDNA ITS and cpDNA rps16 regions for 1586 and 944 samples representing 415 and 397 species, respectively, including Silene and its allies, as well as a species tree analysis including 262 samples representing 243 species. We sampled representatives from all 44 sections recognized in the most recent global revision of the genus. The results support the recognition of three subgenera, i.e., S. subg. Behenantha , S. subg. Lychnis and S . subg. Silene , which is partly in agreement with previous molecular phylogenetic findings and contradicts all previous traditional classifications. Silene sect. Atocion , with a few annual species showing a narrow distribution range in the eastern Mediterranean, is treated as incertae sedis because of its uncertain phylogenetic position, possibly due to exceptionally high substitution rates. Silene subg. Lychnis , weakly supported as sister to the other subgenera, splits into three main clades and includes four sections. Silene subg. Behenantha , which forms a possible sister group in relation to S. subg. Silene , is poorly resolved basally and includes a large number of mostly small clades recognized as 18 sections. In S. subg. Silene , 11 sections are recognized, among which four are broadly circumscribed: S. sect. Auriculatae , S. sect. Sclerocalycinae , S. sect. Silene and S. sect. Siphonomorpha . Silene sect. Acutifoliae and S. sect. Portenses are described here as new taxa, whereas new status or new combinations are proposed for S. sect. Anotites , S. sect. Muscipula , S. sect. Petrocoma , S. sect. Pulvinatae , S. sect. Sclerophyllae and S. sect. Uebelinia . Five new combinations and two new names are proposed for taxa in Silene formerly assigned to Lychnis and Uebelinia . The correct infrageneric nomenclature compatible with the new infrageneric system is provided along with synonymy and type citations. Shortcomings of this study, such as the lack of a morphological diagnostic key and sparse sampling of some large sections, are listed and discussed.
... Acanthophyllum C.A. Meyer species are small, shrub perennial plants with spiny leaves that adapted to deserts, mountains, and temperate areas and are found in sandy or stony hills and rocky slopes. They are important components of the steppe and mountain vegetation in central and southwest Asia (Mahmoudi Shamsabad et al 2012;Pirani et al 2014;Zohary 1973). Acanthophyllum genus is of medical interest due to the cytotoxic properties of many saponins present in its roots. ...
... The genus Acanthophyllum C. A. Mey (Caryophyllaceae) is an important element of subalpine steppe flora in central to south-west Asia and is represented by over 60 species, of which 23 are endemic to Iran (Schiman-Czeika, 1988). The genus includes small, woody base herbaceous perennials with spiny leaves and cushion forms that grow on sandy, stony, or rocky slopes and hills of open habitats (Ghaffari, 2004;Mahmoudi Shamsabad, Vaezi, Memariani, & Joharchi, 2012;Pirani et al., 2014;Schiman-Czeika, 1988). The Irano-Turanian (IT) region is considered the centre of diversification of Acanthophyllum species. ...
... These species belong to section Oligosperma Schischk. (Schiman-Czeika, 1988) and relationships among them are not well resolved using chloroplast and nuclear markers but all three species nested in 'Clade I' of Pirani et al. (2014). The A. laxiusculum differs from A. squarrosum and A. heratense in having pedunculate flowers, and trichome density is used as the distinguishing character between A. squarrosum and A. heratense (Schiman-Czeika, 1988). ...
... In this study, phylogenetic trees and haplotype networks provided no evidence for distinct genetic groups in the A. squarrosum complex, possibly because of incomplete lineage sorting and/or introgression following secondary contacts after speciation. Introgression and hybridization in Caryophyllaceae have been described previously in a number of studies (Fior, Karis, Casazza, Minuto, & Sala, 2006;Petri, Pfeil, & Oxelman, 2013;Pfeil, Toprak, & Oxelman, 2017;Pirani et al., 2014), and had important roles in diversification of Acanthophyllum species (Ghaffari, 2004). ...
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Acanthophyllum squarrosum and two closely related species, A. heratense and A. laxiusculum (Caryophyllaceae), form a complex that covers parts of subalpine steppes of the Irano-Turanian (IT) region. In this study, we explored the genetic structure and phylogeography of this complex based on partial sequences of two chloroplasts (psbA–trnH and rpl32–trnL (UAG)) and two nuclear (EST24 and nrITS) DNA regions. We analysed 80 individuals from eight populations and detected 12 chloroplast haplotypes, 16 and eight nuclear alleles in EST24 and nrITS sequences, respectively. Phylogenetic trees and haplotype networks did not show distinct genetic groups in the complex and this could be explained by incomplete lineage sorting or introgression between species. Divergence time analysis revealed a Quaternary origin for A. squarrosum complex at approximately 1.8 million years ago (Mya) and the neutrality test results indicated that this complex experienced a recent population expansion. AMOVA analysis of the chloroplast regions showed a significant genetic differentiation among populations and low genetic differentiation within populations, but opposite results were found with nuclear markers, implying introgression between A. squarrosum complex populations.
... The genus Dianthus differs from close genera by having bracteoles closely adpressed to calyx (see e.g., Revee 1967, Hernández-Ledesma et al. 2015, Madhani et al. 2018. The monophyly of tribe Caryophylleae Lamarck & Candolle (1806: 386) and some of its large genera such as Dianthus and Acanthophyllum Meyer (1831: 241) are confirmed by both morphological and molecular evidence (Fior et al. 2004, Harbaugh et al. 2010, Greenberg & Donoghue 2011, Pirani et al. 2014. However, some nomenclatural changes, as welle as synonymies are still necessary to make Dianthus as monophyletic (see Greenberg & Donoghue 2011, Harbaugh et al. 2010. ...
Article
The Flora of Turkey includes 88 Dianthus taxa. Some interesting populations belonging were observed in the Sivas province (C-Turkey). On the basis of both morphological and molecural investigations the Sivas population was here described as a new species for the science, named Dianthus hamzaoglui. A diagnosis, detailed description, distribution area, habitat, and IUCN assessment, as well as original photos were provided, as well as a comparison with the related D. burdurensis.
... Caryophyllaceae is a large mainly Holarctic family of approximately 3000 species of herbs and subshrubs, with its diversity center in the Mediterranean and the adjacent family have shown that many of the traditionally defined genera are not monophyletic (Dillenberger & Kadereit, 2014;Pirani et al., 2014;Sadeghian et al., 2015;Madhani et al., 2018). This is also the case for the tribe Caryophylleae, where, based on morphology (connate sepals, stipitate ovary, and presence of two styles), the plant from the Shirkuh Mts. was suspected to belong to. ...
... Madhani et al. (2018), revising tribe Caryophylleae, described three new genera and resurrected one genus. Thus, currently the tribe contains 14 genera As morphological data did not permit assignment of the plants from Shirkuh Mts. to any of the currently recognized genera, we used molecular phylogenetic data to place this taxon within the phylogenetic framework of the tribe Caryophylleae established by Pirani et al. (2014) and Madhani et al. (2018). Hence, by determining the phylogenetic position of the new taxon based on molecular data, we wanted to clarify its taxonomic position. ...
Article
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Although mountain ranges are often recognized as global biodiversity hotspots with a high level of endemism, diversity and biogeographic connections of isolated and weakly explored mountains remain poorly understood. This is also the case for Shirkuh Mts. in central Iran. Here, Yazdana shirkuhensis gen. & spec. nov. (Caryophylleae, Caryophyllaceae) is described and illustrated from the high alpine zone of this mountain. Molecular phylogenetic analyses of nuclear and plastid DNA sequence data show that Yazdana shirkuhensis is related to Cyathophylla and Heterochroa (tribe Caryophylleae). The herein newly described genus and species accentuate the Shirkuh Mts. as a center of endemism, which harbors a high number of narrowly distributed species, mostly in high elevations reaching alpine habitats. As this area is currently not protected, high elevations of Shirkuh Mts. have conservation priority. This article is protected by copyright. All rights reserved.